2HPX

13mer Duplex DNA containing a 4'-oxidized abasic site, averaged structure

Summary for 2HPX

• Entry DOI: 10.2210/pdb2hpx/pdb
• Related: 2HOU
• Descriptor: 5'-D(*CP*CP*AP*AP*AP*GP*(X4A)P*AP*CP*CP*GP*GP*G)-3', 5'-D(*CP*CP*CP*GP*GP*TP*AP*CP*TP*TP*TP*GP*G)-3' (2 entities in total)
• Functional Keywords: abasic site, dna damage, bleomycin, molecular dynamics, dna
• Biological source: synthetic construct; More
• Total number of polymer chains: 2
• Total formula weight: 7852.09

Authors

Chen, J.,Dupradeau, F.Y.,Case, D.A.,Turner, C.J.,Stubbe, J. (deposition date: 2006-07-17, release date: 2007-05-29, Last modification date: 2024-05-01)

Primary citation

Chen, J.,Dupradeau, F.Y.,Case, D.A.,Turner, C.J.,Stubbe, J.
Nuclear magnetic resonance structural studies and molecular modeling of duplex DNA containing normal and 4'-oxidized abasic sites.
Biochemistry, 46:3096-3107, 2007

PubMed Abstract: A 4'-oxidized abasic site (X) has been synthesized in a defined duplex DNA sequence, 5'-d(CCAAAGXACCGGG)-3'/3'-d(GGTTTCATGGCCC)-5' (1). Its structure has been determined by two-dimensional NMR methods, molecular modeling, and molecular dynamics simulations. 1 is globally B-form with the base (A) opposite X intrahelical and well-stacked. Only the alpha anomer of X is observed, and the abasic site deoxyribose is largely intrahelical. These results are compared with a normal abasic site (Y) in the same sequence context (2). Y is composed of a 60:40 mixture of alpha and beta anomers (2alpha and 2beta). In both 2alpha and 2beta, the base (A) opposite Y is intrahelical and well-stacked and the abasic site deoxyribose is predominantly extrahelical, consistent with the reported structures of the normal abasic site in a similar sequence context [Hoehn, S. T., Turner, C. J., and Stubbe, J. (2001) Nucleic Acids Res. 29, 3413-3423]. Molecular dynamics simulations reveal that the normal abasic site appears to be conformationally more flexible than the 4'-oxidized abasic site. The importance of the structure and flexibility of the abasic site in the recognition by the DNA repair enzyme Ape1 is discussed.

PubMed: 17323932
DOI: 10.1021/bi6024269

Experimental method

SOLUTION NMR